Pair-input data are encountered in many applications and have unique properties that need to be taken into account. In this module, we first discuss what pair-input data are and what key characteristics they have, introducing drug-target interactions as an example. We then examine how dependencies emerge between pair-input observations and discuss how those dependencies can be used to characterize pair-input observations. Building on this categorization, we finally explore how to modify performance evaluation methods to obtain reliable estimates of out-of-sample prediction performance for pair-input data. The modifications to the selection of training observations are mathematically formulated.

In this module, we will learn how to determine suitable statistical tests for given machine learning tasks. As an example, we will go through the well-known Wilcoxon test for classifier evaluation. We will also learn about some of the common pitfalls we can fall into if we are not careful in model performance estimation. We see how it is possible to get a very good model performance estimations even though there is no existing pattern in the data. In addition, we will learn how careless feature selection can cause optimistically biased performance estimation in cross-validation. Lastly, we go through the permutation test which allows us to measure the statistical significance of our model performance estimate.